Difference between revisions of "Curation status"
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| align="center" style="background:#f0f0f0;"|'''Pre-build db storage of curated data''' | | align="center" style="background:#f0f0f0;"|'''Pre-build db storage of curated data''' | ||
| align="center" style="background:#f0f0f0;"|'''Curation status source''' | | align="center" style="background:#f0f0f0;"|'''Curation status source''' | ||
+ | | align="center" style="background:#f0f0f0;"|'''Notes/actions''' | ||
|- | |- | ||
− | |'''''C. elegans'''''||'''celegans'''||afp,cfp||none||NA| | + | |'''''C. elegans'''''||'''celegans'''||afp,cfp||none||NA|| |
|- | |- | ||
− | |'''''C. elegans'' other than Bristol'''|| cnonbristol ||afp,cfp||none||NA| | + | |'''''C. elegans'' other than Bristol'''|| cnonbristol ||afp,cfp||none||NA|| |
|- | |- | ||
− | |'''Nematodes other than ''C. elegans'''''||nematode||afp,cfp||none||NA| | + | |'''Nematodes other than ''C. elegans'''''||nematode||afp,cfp||none||NA|| |
|- | |- | ||
− | |'''Non-nematode species'''||nonnematode||afp,cfp||none||NA| | + | |'''Non-nematode species'''||nonnematode||afp,cfp||none||NA|| |
|- | |- | ||
− | |'''Genes studied in this paper'''||genestudied||afp, cfp, tfp||geneace|| | + | |'''Genes studied in this paper'''||genestudied||afp, cfp, tfp||geneace|||| |
|- | |- | ||
− | |'''Newly cloned gene''' || genesymbol ||afp, cfp, jfp||geneace|| | + | |'''Newly cloned gene''' || genesymbol ||afp, cfp, jfp||geneace|||| |
|- | |- | ||
− | |'''Newly created allele'''||extvariation||afp, cfp, tfp, jfp||variation NS||home/acedb/karen/cur_status_sources/vargene_ref.txt| | + | |'''Newly created allele'''||extvariation||afp, cfp, tfp, jfp||variation NS||home/acedb/karen/cur_status_sources/vargene_ref.txt|| |
|- | |- | ||
− | |'''Genetic mapping data'''||mappingdata||cfp, afp||geneace||| | + | |'''Genetic mapping data'''||mappingdata||cfp, afp||geneace|||| |
|- | |- | ||
− | |'''Phenotype analysis''' || newmutant ||cfp, afp, svm ||postgres||postgres| | + | |'''Phenotype analysis''' || newmutant ||cfp, afp, svm ||postgres||postgres|| |
|- | |- | ||
− | |'''Small-scale RNAi'''||rnai||afp, cfp, tfp, svm||citace||postgres| | + | |'''Small-scale RNAi'''||rnai||afp, cfp, tfp, svm||citace||postgres through the paper editor link /~postgres/cgi-bin/paper_editor.cgi|| |
|- | |- | ||
− | |'''Large-scale RNAi'''||lsrnai||afp, cfp, tfp, svm||citace||postgres| | + | |'''Large-scale RNAi'''||lsrnai||afp, cfp, tfp, svm||citace||postgres through the paper editor link /~postgres/cgi-bin/paper_editor.cgi|| |
|- | |- | ||
− | |'''Overexpression phenotype'''||overexpr||afp, cfp, svm||postgres||postgres via transgene-phenotype| | + | |'''Overexpression phenotype'''||overexpr||afp, cfp, svm||postgres||postgres via transgene-phenotype|| |
|- | |- | ||
− | |'''Chemicals'''||chemicals (molecule?) ||afp, cfp||postgres||| | + | |'''Chemicals'''||chemicals (molecule?) ||afp, cfp||postgres|||| |
|- | |- | ||
− | |'''Mosaic analysis'''||mosaic ||afp, cfp||?||| | + | |'''Mosaic analysis'''||mosaic ||afp, cfp||?|||| |
|- | |- | ||
− | |'''Tissue or cell site of action'''|| siteaction ||afp, cfp||?||| | + | |'''Tissue or cell site of action'''|| siteaction ||afp, cfp||?|||| |
|- | |- | ||
− | |'''Time of action''' || timeaction||afp, cfp||?||| | + | |'''Time of action''' || timeaction||afp, cfp||?|||| |
|- | |- | ||
− | |'''Molecular function of a gene product'''||genefunc||afp, cfp||?||| | + | |'''Molecular function of a gene product'''||genefunc||afp, cfp||?|||| |
|- | |- | ||
− | |'''Homolog of a human disease-associated gene.'''|| humdis ||afp, cfp||?||| | + | |'''Homolog of a human disease-associated gene.'''|| humdis ||afp, cfp||?|||| |
|- | |- | ||
− | |'''Genetic interactions''' ||geneint||tfp, afp, cfp||postgres||postgres| | + | |'''Genetic interactions''' ||geneint||tfp, afp, cfp||postgres||postgres|| |
|- | |- | ||
− | |'''Functional complementation'''||funccomp||afp, cfp||?||NA| | + | |'''Functional complementation'''||funccomp||afp, cfp||?||NA|| |
|- | |- | ||
− | |'''Gene product interactions''' ||geneprod||afp, cfp||?||| | + | |'''Gene product interactions''' ||geneprod||afp, cfp||?|||| |
|- | |- | ||
− | |'''New expression pattern for a gene'''|| otherexpr ||afp, cfp,SVM ||postgres||postgres| | + | |'''New expression pattern for a gene'''|| otherexpr ||afp, cfp,SVM ||postgres||postgres|| |
|- | |- | ||
− | |'''Alterations in gene expression by genetic or other treatment'''|| genereg ||afp, cfp||postgres||home/acedb/karen/cur_status_sources/regulation_ref.txt| | + | |'''Alterations in gene expression by genetic or other treatment'''|| genereg ||afp, cfp||postgres||home/acedb/karen/cur_status_sources/regulation_ref.txt|| |
|- | |- | ||
− | |'''Regulatory sequence features'''||seqfeat ||afp, cfp||?||| | + | |'''Regulatory sequence features'''||seqfeat ||afp, cfp||?|||| |
|- | |- | ||
− | |PFM, PWM|| matrices||afp, cfp||? ||| | + | |'''PFM, PWM'''|| matrices||afp, cfp||?|||| |
|- | |- | ||
− | |'''Microarray'''|| microarray ||afp, cfp||citace?||/karen/cur_status_sources/microarray_ref.txt| | + | |'''Microarray'''|| microarray ||afp, cfp||citace?||/karen/cur_status_sources/microarray_ref.txt|| |
|- | |- | ||
− | |in vitro ''Protein analysis''|| invitro|| SVM?||?||| | + | |'''in vitro ''Protein analysis'''''|| invitro|| SVM?||?|||| |
|- | |- | ||
− | |'''Domain analysis''' || domanal (populated with information previously in "structureinformation")||||?||NA| | + | |'''Domain analysis''' || domanal (populated with information previously in "structureinformation")||||?||NA|| |
|- | |- | ||
|'''Covalent modification'''|| covalent||||?||NA|| | |'''Covalent modification'''|| covalent||||?||NA|| | ||
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|'''Structural information'''|| structinfo||||?||NA|| | |'''Structural information'''|| structinfo||||?||NA|| | ||
|- | |- | ||
− | |'''Mass spectrometry'''|| massspec||afp, cfp||Hinxton||| | + | |'''Mass spectrometry'''|| massspec||afp, cfp||Hinxton|||| |
|- | |- | ||
− | |'''''C. elegans'' antibodies'''|| antibody ||tfp||postgres?||/karen/cur_status_sources/antibody_ref.txt| | + | |'''''C. elegans'' antibodies'''|| antibody ||tfp||postgres?||/karen/cur_status_sources/antibody_ref.txt|| |
|- | |- | ||
− | |'''Integrated transgenes'''||transgene||tfp, jfp ||postgres||postgres| | + | |'''Integrated transgenes'''||transgene||tfp, jfp ||postgres||postgres|| |
|- | |- | ||
− | |'''Transgenes used as tissue markers'''|| marker||afp, cfp||postgres||postgres| | + | |'''Transgenes used as tissue markers'''|| marker||afp, cfp||postgres||postgres|| |
|- | |- | ||
− | |'''Gene structure correction''' || structcorr (this use to be two different fields)||?|||| | + | |'''Gene structure correction''' ||structcorr (this use to be two different fields)||?|||||| |
|- | |- | ||
− | |'''Sequencing mutant alleles''' ||seqchange ||||||| | + | |'''Sequencing mutant alleles''' ||seqchange ||afp, cfp|||||| |
|- | |- | ||
− | |'''New SNPs'''||newsnp||||||| | + | |'''New SNPs'''||newsnp||afp, cfp|||||| |
|- | |- | ||
− | |'''Ablation data'''||ablationdata ||||||| | + | |'''Ablation data'''||ablationdata ||afp, cfp|||||| |
|- | |- | ||
− | |'''Cell function'''||cellfunc||||||| | + | |'''Cell function'''||cellfunc||afp, cfp||||||| |
|- | |- | ||
− | |'''Phylogenetic data'''||phylogenetic||||||N/A|| | + | |'''Phylogenetic data'''||phylogenetic||afp, cfp||||N/A|| |
|- | |- | ||
− | |'''Other bioinformatics analysis'''||othersilico||||||N/A|| | + | |'''Other bioinformatics analysis'''||othersilico||afp, cfp||||N/A|| |
|- | |- | ||
− | |'''Supplemental materials'''||supplemental||||||| | + | |'''Supplemental materials'''||supplemental||afp, cfp|||||| |
|- | |- | ||
− | |'''Comment'''||nocuratable||||||| | + | |'''Comment'''||nocuratable||afp, cfp|||||| |
|- | |- | ||
− | |'''Feedback'''||comment||||||| | + | |'''Feedback'''||comment||afp, cfp|||||| |
|- | |- | ||
− | |'''Strain'''||?||jfp | + | |'''Strain'''||?||jfp||textpresso (GSA), postgres-afp table|||| |
|- | |- | ||
− | |'''Rearrangements'''||?||jfp | + | |'''Rearrangements'''||?||jfp||textpresso (GSA), postgres-afp table|||| |
|- | |- | ||
− | |'''Cell/anatomy terms and synonyms'''||?||jfp | + | |'''Cell/anatomy terms and synonyms'''||?||jfp ||textpresso (GSA), postgres-afp table||/karen/cur_status_sources/anatomy_ref.txt|| |
− | /anatomy_ref.txt| | ||
|- | |- | ||
− | |'''New phenotype'''||?||jfp | + | |'''New phenotype'''||?||jfp||textpresso (GSA), postgres-afp table||?|| |
|- | |- | ||
|} | |} | ||
− | afp = Author first pass | + | afp = Author first pass table |
− | cfp = Curator first pass | + | cfp = Curator first pass table |
− | tfp = Textpresso first pass | + | tfp = Textpresso first pass table |
− | jpf = Journal first pass | + | jpf = Journal first pass form = afp first pass table |
SVM = Support Vector Machine | SVM = Support Vector Machine |
Revision as of 19:48, 8 June 2011
A number of pages have been set up to keep track of the papers that have been flagged and curated for respective datatypes; unfortunately not all datatypes are easily tracked and so the information in regards to whether or not a paper has been curated for that datatype may not be up to date. Eventually this page should point to a table that is a comprehensive display of the curation status of a given paper as well as a table that can show how far we've come along in curating the nematode published corpus in our database.
Current status forms
Datatypes, curation storage and source for generating curation status
Data type | afp PGdb name | Flagging method(s) | Pre-build db storage of curated data | Curation status source | Notes/actions |
C. elegans | celegans | afp,cfp | none | NA | |
C. elegans other than Bristol | cnonbristol | afp,cfp | none | NA | |
Nematodes other than C. elegans | nematode | afp,cfp | none | NA | |
Non-nematode species | nonnematode | afp,cfp | none | NA | |
Genes studied in this paper | genestudied | afp, cfp, tfp | geneace | ||
Newly cloned gene | genesymbol | afp, cfp, jfp | geneace | ||
Newly created allele | extvariation | afp, cfp, tfp, jfp | variation NS | home/acedb/karen/cur_status_sources/vargene_ref.txt | |
Genetic mapping data | mappingdata | cfp, afp | geneace | ||
Phenotype analysis | newmutant | cfp, afp, svm | postgres | postgres | |
Small-scale RNAi | rnai | afp, cfp, tfp, svm | citace | postgres through the paper editor link /~postgres/cgi-bin/paper_editor.cgi | |
Large-scale RNAi | lsrnai | afp, cfp, tfp, svm | citace | postgres through the paper editor link /~postgres/cgi-bin/paper_editor.cgi | |
Overexpression phenotype | overexpr | afp, cfp, svm | postgres | postgres via transgene-phenotype | |
Chemicals | chemicals (molecule?) | afp, cfp | postgres | ||
Mosaic analysis | mosaic | afp, cfp | ? | ||
Tissue or cell site of action | siteaction | afp, cfp | ? | ||
Time of action | timeaction | afp, cfp | ? | ||
Molecular function of a gene product | genefunc | afp, cfp | ? | ||
Homolog of a human disease-associated gene. | humdis | afp, cfp | ? | ||
Genetic interactions | geneint | tfp, afp, cfp | postgres | postgres | |
Functional complementation | funccomp | afp, cfp | ? | NA | |
Gene product interactions | geneprod | afp, cfp | ? | ||
New expression pattern for a gene | otherexpr | afp, cfp,SVM | postgres | postgres | |
Alterations in gene expression by genetic or other treatment | genereg | afp, cfp | postgres | home/acedb/karen/cur_status_sources/regulation_ref.txt | |
Regulatory sequence features | seqfeat | afp, cfp | ? | ||
PFM, PWM | matrices | afp, cfp | ? | ||
Microarray | microarray | afp, cfp | citace? | /karen/cur_status_sources/microarray_ref.txt | |
in vitro Protein analysis | invitro | SVM? | ? | ||
Domain analysis | domanal (populated with information previously in "structureinformation") | ? | NA | ||
Covalent modification | covalent | ? | NA | ||
Structural information | structinfo | ? | NA | ||
Mass spectrometry | massspec | afp, cfp | Hinxton | ||
C. elegans antibodies | antibody | tfp | postgres? | /karen/cur_status_sources/antibody_ref.txt | |
Integrated transgenes | transgene | tfp, jfp | postgres | postgres | |
Transgenes used as tissue markers | marker | afp, cfp | postgres | postgres | |
Gene structure correction | structcorr (this use to be two different fields) | ? | |||
Sequencing mutant alleles | seqchange | afp, cfp | |||
New SNPs | newsnp | afp, cfp | |||
Ablation data | ablationdata | afp, cfp | |||
Cell function | cellfunc | afp, cfp | |||
Phylogenetic data | phylogenetic | afp, cfp | N/A | ||
Other bioinformatics analysis | othersilico | afp, cfp | N/A | ||
Supplemental materials | supplemental | afp, cfp | |||
Comment | nocuratable | afp, cfp | |||
Feedback | comment | afp, cfp | |||
Strain | ? | jfp | textpresso (GSA), postgres-afp table | ||
Rearrangements | ? | jfp | textpresso (GSA), postgres-afp table | ||
Cell/anatomy terms and synonyms | ? | jfp | textpresso (GSA), postgres-afp table | /karen/cur_status_sources/anatomy_ref.txt | |
New phenotype | ? | jfp | textpresso (GSA), postgres-afp table | ? |
afp = Author first pass table
cfp = Curator first pass table
tfp = Textpresso first pass table
jpf = Journal first pass form = afp first pass table
SVM = Support Vector Machine